Profile

Expert in applied bioinformatics with 8+ years of experience in providing transparent and reproducible solutions for diverse areas of biological and medical research. Deep knowledge of underlying issues in need of bioinformatics support. Experience includes genetic epidemiology of rare diseases, integrative omics analysis of data from cancer tissue and immune cells, microarray analysis, preprocessing to final analysis of NGS output. The integrative analysis, performed during phd, encompassed, gene expression, copy number variation, promoter methylation and histone occupancy data. Integrative analysis of proteomics, clinical and brain imaging data. Focused on keeping at the forefront of the latest within computational omics analysis. I have emotional intelligence, strong communication skills and am a great teammate. I am dynamic and work very hard to achieve the intended result which has been decided from the start on time. I am not pretentious. I speak my mind and make it safe for others to do so. My collegues say about me that I am hardworking, joyful and problemsolving.

Objective

To further develop my skills in developing reproducible bioinformatics pipelines and contribute to improved insight into cancer development and treatment through the development of supporting computational infrastructure and algorithms. To further develop my knowledge of and skills in applying AI and ML in piplines. To share attained knowledge.

Relevant competences

• Analysis of proteomics data
• Integrative omics analysis
• Pathway and network analysis
• shell, (Python), R, git, Github, Nextflow, Docker
• scientific communication and writing

Researacher bioinformatics

Sahlgrenska ac., Univeristy of Gothenburg

Göteborg, Sweden

2022 - 2020

• Developed a pipeline of rscripts to perform pathway and correlation network analysis of cord blood plasma proteomics data.
• Worked with Rstudio and the R package collections Bioconductor and Tidyverse. Reports where generated with R notebooks and the R package Bookdown. Github and
• GitKraken is used for code version control. Recently applied R packages are DEqMS for differential expression analysis of mass spectrometry data, WGCNA for proteins correlation analysis and ReactomeGSA for pathway analysis

Senior engineer bioinformatics

Norwegian Sequencing Center

University of Oslo, Norway

2017 - 2014

• Set up server infrastructure for NGS data handling. Manged NGS file servers, user access and data delivery.
• Examples of downstream analysis: Blasted an exon sequence against multiple assembled fish genomes to look for systematic loss in phylogeny. Analyzed bacterial methylomes, sequenced with Pacbio in, respect to virulens.
• System setup, user management, data preprocessing, delivery and down stream analysis of Illumina and Pacbio sequence data at the Norwegian DNA sequencing center. Workflow automation with cron and make

Principal engineer

Bioinformatics core facility

Rikshospitalet HF, Norway

2008 - 2007

• Microarray gene expression analysis

Research assistant

Human Genetics division

Children’s Hospital of Philadelphia, USA

2007 - 2006

• Bash and scripting for data wrangling and testing Solar, Plink, TDT, Merlin, STATA, SAS, R

Senior research assistant

Dept. of genetic epidemiology

Nemours Hospital for Children, USA

2005 - 2004

• Used software for genetic linkage and association studies of diseases/syndroms Velocardiofacial Syndrome, ADHD, Neuroblastoma, Osteoporosis, Cornelia de Lange’s syndrome and Myopia • Solar, Plink, TDT, Merlin, STATA, SAS, R

Database coordinator

Human Genetics division

Children’s Hospital of Philadelphia, USA

2004 - 2002

• Manged a database for SNP information Progeny2000

R for reprodicible scientific programming

Software carpentry

Oslo Norway

2018 - 2017

Version controlling with git and github

Software carpentry

Oslo Norway

2018 - 2017

Unix

Software carpentry

Oslo Norway

2018 - 2017

PhD bioinformatics

Medical faculty, University of Oslo

Oslo, Norway

2012 - 2007

• PhD project with thesis title: Integrative epigenome analysis. Scripts developed in R and The Genomic Hyperbrowser was used to study the dependencies and select genes, based on genomic, epigenomic and transcriptomic alterations in samples from osteosarcoma and immune cells. The gene expression, promoter methylation and DNA copy number data were acquired by oligonucleotide microarray technology, and the histone modification data was acquired by technology based on chromatin immune precipitation and next generation sequencing, ChIP-seq.
• Developed and R package for clustering of genomic tracks.

Master of Science in Bioinformatics

Chalmers University of Technology

Gothenburg, Sweden

2001 - 2000

Master of Science in Molecular biology

University of Gothenburg /Uppsala

Göteborg/Uppsala, Sweden

1999 - 1993

The proteome signature of cord blood plasma with high hematopoietic stem and progenitor cell count

Stem Cell Research

N/A

2022

• Authored with Anders K.Nilsson, Annika Thorsell, Sofia Frändberg,Helena Barreto Henriksson, Camilla Hesse, Gunnel Hellgren, Pia Lundgren, AnnHellström

ClusTrack: Feature Extraction and Similarity Measures for Clustering of Genome-Wide Data Sets

Plos One

N/A

2015

• Authored with Geir Kjetil Sandve, Egil Ferkingstad and Eivind Hovig

The Genomic HyperBrowser: inferential genomics at the sequence level

Genome biology

N/A

2010

• Authored with Geir K Sandve, Sveinung Gundersen, Ingrid K Glad, Lars Holden, Marit Holden, Knut Liestøl, Trevor Clancy, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tøstesen, Arnoldo Frigessi & Eivind Hovig

Preprocessing of NGS output

FASTQC, etc

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Downstream analysis of NGS output

Gene centric(DEG), GO and pathway centric, correlation module centric

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Programming

R, shell, Python

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Version control

git,Github

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Swedish (native)

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English (native)

N/A

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Norwegian (good)

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Pangenomes Evolution and Computation

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Tutoring PhD students

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